Genome Digest

Rainbow trout

TOM OLIVO (FLY FISHING PORTRAITS0Species: Oncorhynchus mykiss
Genome size: 1.9 billion base pairs

The rainbow trout (Oncorhynchus mykiss) is raised in aquaculture the world over and is among the most studied fish species. Scientists in France have now sequenced its genome, uncovering evidence of whole-genome duplications that were landmarks of vertebrate evolution and the divergence of teleost fish. The team uncovered and examined two copies of the ancestral salmonid genome within the rainbow trout genome, and used it to infer evolutionary relationships between the fish.

“Due to a relatively recent WGD [whole-genome duplication], the rainbow trout thus provides a unique opportunity to better understand the early steps of gene fractionation,” the rearrangement of the genome following duplication, the researchers wrote in Nature Communications this week (April 22). They added that their results challenge the hypothesis that whole-genome duplications are “followed by massive and rapid genomic reorganizations and gene deletions.”

Segmented RNA virus

Yellow fever virus, which is related to one segment of JMTVCDCSpecies: Jingmen tick virus (JMTV)

Researchers from the Chinese Center for Disease Control and Prevention in Beijing and their colleagues described in PNAS this week (April 21) a previously unidentified segmented RNA virus of ticks called Jingmen tick virus (JMTV). JMTV contains two segments from an unsegmented flavivirus, plus two other segments of unknown origins. The tick-borne virus is distributed across China, the researchers reported, inhabiting Rhipicephalus and Haemaphysalis species in particular.

“To our knowledge, JMTV is the first example of a segmented RNA virus with a genome derived in part from unsegmented viral ancestors,” the researchers wrote in their paper. “Collectively, these results demonstrate the remarkable diversity of viral genome structures as well as a previously unidentified evolutionary link between unsegmented and segmented viruses.”

See “Going Viral,” The Scientist, September 2013.

Pathogenic fungus

DUKE UNIVERSITYSpecies: Cryptococcus neoformans var. grubii
Genome size: 19 million base pairs

An international team led by investigators at the Pasteur Institute in Paris, Duke University in Durham, North Carolina, and the Broad Institute in Cambridge, Massachusetts, published whole-genome and transcriptome sequences for the fungal pathogen Cryptococcus neoformans var. grubii in PLOS Genetics this month (April 17). C. neoformans var. grubii infection can cause meningoencephalitis in immunocompromised patients and is responsible for some 600,000 deaths worldwide each year, the researchers noted.

In its analysis, the team uncovered molecular signatures of the pathogen’s virulence and ability to adapt to changing conditions. “Cryptococcus neoformans has to cope with a large number of different stresses and probably needs a very flexible metabolism,” Pasteur Institute mycologist Guilhem Janbon, who led the work, said in a statement. “It is tempting to hypothesize that its complex RNA metabolism provides a mechanism to achieve such flexibility.”

Study coauthor Christina Cuomo, who leads the Broad Institute’s Fungal Genome Sequencing and Analysis group, added: “This genome will serve as an important reference for the field, to enable a wide range of analysis from examining individual genes to comparing the genomes and transcriptomes of other strains and conditions.”